GENETIC AND GENOMIC TAXONOMY OF HUMAN DISEASE

GENETIC AND GENOMIC TAXONOMY OF HUMAN DISEASE

The philosophy of disease is complex and reflects the way an abnormal body state is perceived and understood against the background of sociocultural, psychological, and biomedical interpretation. During the late phase of the last millennium, new scientific discoveries in genetics offered entirely new approaches[1]. Nevertheless, environmental and sociocultural factors remain important in influencing the outcome of disease. The psychological and biomedical factors provide the innate framework for generating and developing symptoms and signs of the disease, depending on the pathology. On this basis, a “disease” could be best defined as an “overall perception of an abnormal body state and appreciation of the ensuing psychological and physical impact.”

Historically, clinical practice has always faced its inability to differentiate events that mediate the disease process from resulting clinical, biochemical, and pathological changes. Rapid advances in  biomedical sciences, particularly genomics, have opened entirely new horizons[2][3]. However, despite having made tremendous advances, clinicians continue to rely on phenotypical manifestations of the disease process to define most diseases. Inevitably, this approach often obscures the underlying mechanisms; thus a clinician may fail to identify significant heterogeneity. Concerns have been raised that most human disease provides only “insecure and temporary conceptions”[4]. Apart from infectious diseases, there are alarmingly few diseases that have a truly mechanism-based nomenclature.

The classification of human disease depends on several factors, ranging from perception and analysis of symptoms, sociocultural interpretation of varied manifestations of the disease, and biological considerations,to therapeutic  interventions.  Conventionally,  “disease”  refers  to  a  particular organ or system dysfunction resulting from one or more causative factors such as physical trauma, infection, exposures to a toxic substance, or malnutrition. A large number of diseases remain unaccounted for due to the lack of a clear explanation for their underlying mechanisms. Terms like degenerative or autoimmune disorders are not uncommonly used to describe an organ-system dysfunction. However,whether there is a “cause and effect” relationship remains unclear. Nevertheless, associated pathological changes often provide a firm and precise basis to categorize a disease or disorder. This has helped in delineating distinct categories of diseases such as immunological and metabolic diseases.

Developments in genetics and molecular biology have provided a vast amount of data and information to support the view that most human diseases have a significant genetic component. Characterization of the genetic determinants of disease provides remarkable opportunities for clinical medicine through an improved understanding of pathogenesis, diagnosis, and therapeutic options. An understanding of the genetic basis of human disease has opened the way for a new taxonomy of human disease that will be free from limitations and bias in developing diagnostic criteria related to events that are often secondary and peripheral to its cause[3]. For instance, genetic information has allowed us to identify distinct forms of diabetes mellitus: defining an auto-immune form associated with highly diverse and complex human leukocyte antigens (HLA) and other inherited factors that affect both expression and modification of gene products in mediating the adult form of the disease[5]. Similarly, many genetically determined molecules and pathways have been characterized that are crucial in the pathogenesis of bronchial asthma[6]. It is now widely believed that a clearer understanding of the mechanisms and pathways of a disease will assist us in delineating distinct disease subtypes and may resolve many questions relating to variable disease symptoms, progression, and response to therapy. This might help in revising the current diagnostic criteria. Eventually, genetics may contribute a new taxonomy of human disease in clinical practice.

Although genetics is acknowledged to be an important aspect of understanding the pathogenesis of disease, the genetic classification  of human disease has not yet received full recognition. There is ample evidence in support of the argument that genetic factors are probably associated with all human diseases except for trauma (Figure 20.1). However, underlying genetic and genomic factors such as genetically determined connective-tissue disorders, host-response to infection, and tissue damage or inflammation could influence the outcome of trauma. Various categories of genetic disorders are considered to be rare, with a tendency to be included under the broad title of “organ-system diseases.” Often these are listed as simply etiological factors rather than as a distinct disease category. This concept and approach is now rapidly being outdated, however, and replaced with new classes of diseases. This progress is seriously hampered by the lack of formal education at all levels and integration of appropriate technologies into the modern medical diagnostic and therapeutic infrastructure.

Figure 20.1 Genetic factors in human  disease.

Table 20.1 THE CLASSIFICATION OF GENETIC  DISORDERS

Chromosomal: Numericalaneuploidy

Structuraldeletion, duplication, inversion, isochromosome

Ring chromosome, reciprocal or Robertsonian  translocation

Mendelian: Autosomal recessive

Autosomal dominant

X-linked recessive

X-linked dominant

Epigenetic: Imprinting/parent of origin effect; indirect influence on gene function
Oligogenic: Distinct phenotype due to 2 or more  genes
Polygenic:   Environmental interaction with several hundreds of low-risk alleles,    genetic polymorphisms, and genomic copy number  variations
Mitochondrial: Deletion; point mutations; polymorphic variants in  mtDNA
Genomic variation:

Copy number variation; single-nucleotide  polymorphisms

Traditionally, genetic diseases are classified as chromosomal (numerical or structural), Mendelian or single-gene disorders, multifactorial/polygenic complex diseases or congenital anomalies, and diseases associated with specific mitochondrial gene mutations (Table 20.1). Apart from chromosomal disorders, essentially all genetic disorders result from some form of alteration or mutation occurring in a specific gene (single-gene diseases) or involving multiple loci spread across the human genome (polygenic disorders). The major impact of chromosomal disorders occurs before birth and inflicts a serious health burden throughout childhood and during the early years of life (Figure 20.2). On the other hand, single-gene diseases can pose a real medical and health burden from the perinatal period to adult age, with a peak around mid-childhood. In contrast, the polygenic/multifactorial diseases tend to present late, except for developmental anomalies that will require active multidisciplinary care during a child’s early life. A brief description of the major types of genetic diseases is included here. Any leading medical genetics textbook will contain a detailed description of all these group of genetic disorders.

Figure 20.2 Distribution of different genetic disorders in various age groups. Adapted with permission from Principles of Medical Genetics by Thomas D. Gelehrter, Francis S. Collins, and David Ginsburg[1].

CHROMOSOMAL DISORDERS

The entire human genome is spread around 23 pairs of chromosomes, including one pair specifically assigned to male (XY) or female (XX) gender, designated the “sex-chromosome pair.” The chromosomal constitution  of man is complex and comprises variable amounts of euchromatin and heterochromatin that exhibit with a characteristic “banding-pattern,” and is essential   for   the   physical   and   distinctive   appearance   of   a  particular chromosome. Typically, a chromosome pair includes two homologues, each comprising a short arm (p) and a long arm (q) separated by the central heterochromatin-G-C–rich region designated the “centromere.” A detailed account of the chromosome structure and fundamental changes that occur during meiosis and mitosis can be found in any leading textbook on basic genetics.

Chromosomal disorders are essentially disorders of the genome resulting from either loss or addition of a whole chromosome (aneuploidy) or parts of chromosomes (structural). A chromosome abnormality results in major disturbance in the genomic arrangement, since each chromosome or part thereof consists of thousands of genes and several non-coding polymorphic DNA sequences. The physical manifestations of chromosome disorders are often quite striking, characterized by growth retardation, developmental delay, and a variety of somatic abnormalities. Many chromosomal syndromes are now recognizable. The diagnosis and genetic management of these disorders fall within the scope of the sub-specialty “clinical cytogenetics.”

The management of chromosomal disorders requires a coordinated and dedicated team approach involving a wide range of clinicians and health professionals. A typical example is Down syndrome, resulting from either three copies of chromosome 21 (trisomy) (Figure 20.3) or an addition to the long arm of chromosome 21, usually resulting from an unbalanced meiotic rearrangement of a parental chromosomal translocation between chromosome 21 and one of the other acrocentric (centromere located at the end) chromosomes (Robertsonian translocation). Down syndrome occurs in about one in 800 live births and increases in frequency with advancing maternal age. It is characterized by growth and developmental delay, moderate to severe mental retardation, and the characteristic facial appearance recognized with upward-slanting eyes. A major cause of death in these individuals is associated congenital heart defects that can complicate the clinical management in a significant proportion of Down syndrome cases. Prenatal diagnosis and prenatal assessment of the maternal risk for Down syndrome employing a variety of imaging and biochemical parameters is now established clinical and public health practice in most countries.


Figure 20.3 Karyotype of a female (XX) with Down syndromenote trisomy 21.

Clinically significant chromosome abnormalities occur in nearly 1% of live-born births and account for about 1% of pediatric hospital admissions and 2.5% of childhood mortality[7]. The loss or gain of whole chromosomes is often incompatible with survival, and such abnormalities are a major cause of spontaneous abortions or miscarriages. Almost half of the spontaneous miscarriages are associated with a major chromosomal abnormality. It is estimated that about a quarter of all conceptions may suffer from major chromosome problems, because approximately 50% of all conceptions may not be recognized as established pregnancies, and 15% of these end in a miscarriage. Essentially, the major impact of chromosomal disorders occurs before birth or during early life (Figure 20.2).

The delineation of rare and uncommon chromosomal disorders has been crucial in the gene-mapping of several Mendelian  (single-gene) disorders such as the X-linked Duchenne muscular dystrophy and type 1 neurofibromatosis. The chromosomal regions involved in deletion, duplication, inversion, and break points involved in a complex chromosomal rearrangement provide an important clue and assist the keen researcher in focusing on genes located within the chromosomal segment.

MENDELIAN (SINGLE-GENE) DISORDERS

About 4,000 human diseases are caused by mutations in single genes, and these constitute a major health burden. Single-gene disorders account for approximately 5–10% of pediatric hospital admissions and childhood mortality. The major impact of these disorders occurs in the newborn period and early childhood. However, these also constitute a significant  proportion of adulthood diseases, notably late-onset neurodegenerative diseases and various forms of familial cancer. Although the majority of single-gene diseases are rare, some are relatively common and pose a major health problem. For example, familial hypercholesterolemia, a major predisposing factor in premature coronary artery disease, occurs in one in 500 people. Other good examples would be familial breast and colorectal cancers, which affect approximately one in 300. Some single-gene disorders are specific for certain populations, like Tay-Sachs disease among Ashkenazi Jews, or cystic fibrosis in Caucasians, thalassemias among people from Southeast Asia and the Mediterranean countries, and sickle-cell disease in people of Western African origin. Techniques in molecular biology have enabled the characterization of a number of mutated genes. Sickle-cell disease was the first single-gene disorder to be defined at the molecular level. This has revolutionized the diagnosis and management of these disorders. The single- gene disorders are inherited in a simple Mendelian manner, and hence justifiably called “Mendelian disorders.” The genetic transmission of altered genes or traits follows principles set out by the Austrian monk  Gregor Mendel in 1865, based on his seminal work on garden pea plants[8]. Mendel inferred that “those characteristics that are transmitted entire, or almost unchanged by hybridization, and therefore constitute the characters of the hybrid, are termed dominant, and those that become latent in the process, recessive.”


Figure 20.5 A pedigree with an X-linked dominant disordernote absence of “male–male” transmission; all daughters of an affected male would be heterozygous and thus could be symptomatic. Adapted with permission from Principles of Medical Genetics by Thomas D. Gelehrter, Francis S. Collins, and David Ginsburg[1].


Figure 20.6 The “Gaussian” bell-shaped curve to illustrate “genetic threshold,”indicated by liability in the general population (shown in black). A shift to the right (in gray) indicates increased liability in first-degree relatives with an increased risk of recurrence.With permission from Oxford University Press, U.K.[9].

Identification of any such disorder or condition is important in assessing risks to close relatives. A comparison of general population and multiple cases in a family would indicate a shift of the bell-shaped Gaussian curve tothe right, reflecting a lowered threshold with an increased incidence (Figure 20.6). The precise additional risk would dependon the degree of relationship with the index case in the family. In addition, the gender of the index case is also important in assessing the liability. The genetic liability is estimated to be greater if the index case is of the gender with lowest incidence. For example, in the case of pyloric stenosis, greater risk would be applicable if the index case were a female, which carries the lowest birth prevalence.Finally,   recurrence   risks   for   a   given   population   group are estimated to equal the square root of the birth incidence. For instance, birth incidence of ventricular septal defect is approximately three per 1000, the recurrence risk to a first-degree relative, such as the next child, would be the square root of 0.003, or 3%. These figures are useful in giving a family genetic counseling following the birth of a child with a congenital anomaly.

This group of diseases poses the challenge of working out the mechanisms that determine the additive or interactive effects of many genes creating predisposition to diseases, which in turn manifest only in the presence of certain environmental factors. It is hoped that a combination of molecular genetic approaches, gene mapping, and functional genomics will enable a clearer definition of these genetic diseases. Several sections in this book will address this issue at length and focus on specific disease groups and systems.

MITOCHONDRIAL GENETIC DISORDERS

Apart from nuclear DNA (nDNA), a small proportion of DNA is also found in mitochondria in the cytoplasm of cells (mtDNA). Each cell contains 2–100 mitochondria, each of which contains 5–10 circular chromosomes. The 16.5kb mtDNA molecule is free from any non-coding intronic regions and encodes two ribosomal RNA (rRNA) genes, 22 transfer RNAs (tRNA), and 13 polypeptides that are parts of multi-subunit enzymes involved in oxidative phosphorylation (see also Chapter 9; Figure 20.7). In comparison to the nuclear DNA, the mtDNA is 20 times more prone to recurrent mutations, resulting in generation of mutagenic oxygen radicals in the mitochondria. The inheritance of mtDNA is exclusively maternal, due to its cytoplasmic location. The mature sperm head contains very little mtDNA, since it is almost completely lost during the fertilization process, apparently with the loss of the tail that carried the bulk mtDNA in the cytoplasm. Due to the wholly maternal cytoplasmic location, only females can transmit mitochondrial diseases to their offspring of either gender (see Figure 20.7).

Figure 20.7 The human mitochondrial DNA molecule with examples of point mutations with their associated clinical phenotypes.Adapted from Neurogenetics by Stefan-M. Pulst, Oxford University Press, New York, 2000, with permission[10].

Figure 20.8 Pedigree of a family with mitochondrial encephalopathy with ragged-red muscle fibers (MERRF)—note segregation of different features with variable severity in the affected family members.

Since mtDNA replicates separately from the nuclear DNA, and mitochondria segregate in daughter cells independently of the nuclear chromosomes (replicative segregation), the proportion of mitochondria carrying the mtDNA mutation can differ among somatic cells. This mitochondrial heterogeneity is also called heteroplasmy and plays an important part in the variable and tissue-specific phenotype of mitochondrial disease. Since different tissues have varying degrees of dependence on oxidative phosphorylation,  with heart, muscle, and central nervous system being the most dependent, the common manifestations of mitochondrial disease include cardiomyopathy, myopathy, and encephalopathy (see Figure 20.1). Furthermore, oxidative phosphorylation declines with age, probably related to the accumulation of successive mtDNA mutations. Thus the clinical phenotype in a mitochondrial disease is not simply or directly related to mtDNA genotype, but reflects several factors, including the overall capacity for oxidative phosphorylation determined by mtDNA and nuclear DNA genes, the accumulation of somatic mtDNA mutations and degree of heteroplasmy, tissue-specific requirements of oxidative phosphorylation, and age.

Several mitochondrial diseases have now been characterized (Table 20.2). One of the best-characterized is Leber’s hereditary optic neuropathy (LHON), which exclusively affects males. There is loss of central vision secondary to optic nerve degeneration. The vision loss usually occurs in the patient’s 20s and can progress rapidly in some men. Eleven different missense mtDNA mutations in three different mitochondrial genes encoding respiratory chain enzyme subunits have been described. The phenotype in other mitochondrial diseases tends to include a combination of heart, muscle, and central nervous system manifestations, with considerable intra-/inter-familial variability for the same mtDNA mutation. In addition, mitochondrial dysfunction can be part of the phenotype in some Mendelian diseases where the mutant gene- product presumably has a pathogenic influence on the mitochondrially mediated metabolic pathway. Examples of this are the autosomal recessive respiratory enzyme disorders. Genetic counseling and decision for prenatal diagnosis can be difficult in mitochondrial disorders due to difficulty in predicting the phenotype in the affected pregnancy.

Finally, a high degree of sequence variation (polymorphism) is known to occur in the non-coding region of the mitochondrial chromosome (the D- loop). This polymorphism has been used in anthropological and evolutionary studies to trace the origins and links of human populations. In addition, this information has been applied in forensic analysis as well, to match maternal grandparents’ mtDNA with an orphaned child whose parents have “disappeared” during war, a natural disaster, or in mysterious circumstances.

Table 20.2 GENETIC CLASSIFICATION OF MITOCHONDRIAL DISORDERS

GENOMIC DISORDERS

Recent advances in molecular genetics have enabled us to identify specific groups of disorders that result from characteristic mechanisms involving specific areas of the human genome. Often, these do not conform to the standard basic principles of genetics.A broad term,genomic disorders, has been coined to describe these conditions (Table 20.3)[11].

A number of hereditary disorders present with complex genetic pathology that do not follow the conventional principles of inheritance as outlined in the previous sections. There is now overwhelming evidence within these disorders that indicates unusual mechanisms suggesting “nontraditional inheritance.” The mechanisms involve certain genomic regions that  directly or indirectly influence regulation and expression of one or more genes manifesting in complex phenotypes. Currently, some of these disorders are listed either as chromosomal or as single-gene disorders.

Table 20.3 CLASSIFICATION OF GENOMIC  DISORDERS

Disorders of genomic imprinting (epigenetic  diseases)

Disorders of genome architecture (loss or gain of variable genomic segments)

Tri-nucleotide repeat disorders (variable number of nucleotide repeats with effect on gene function/ expression)

Genomic variation (copy number variation; single-nucleotide   polymorphisms)

DISORDERS OF GENOMIC IMPRINTING: EPIGENETIC DISEASES

The term epigenetics refers to heritable factors that affect gene expression without any change in the gene coding-sequence. These factors could be operational either during meiosis or mitosis and are often selective and preferential on the basis of their “parent of origin.” The term imprinting is commonly used to describe this important biological mechanism that is recognized to influence wide-ranging physical and molecular phenotypes. Numerous human diseases have now been confirmed to  result from epigenetic changes in various parts of the genome. The term epigenetic diseases(or genomic imprinting disorders) refers to this group of diseases.Basic  mechanisms  related  to  the  phenomenon  of  epigenetics  or epigenomics are reviewed separately (see also Chapter 4).

Epigenetic initiation and silencing is regulated by the complex interaction of three systems, including DNA methylation, RNA-associated silencing, and histone modification[12]. The relationship between these three components is vital for the expression or silencing of genes (Figure 20.8). Disruption of one or another of these interacting systems can lead to inappropriate expression or silencing of genes, leading to “epigenetic diseases.” Methylation of the C5 position of cytosine residues in DNA has long been recognized as an epigenetic silencing mechanism of fundamental importance[13]. The methylation of CpG sites within the human genome is maintained by a number of DNA methyltransferases (DNMTs) and plays multifaceted roles in the silencing of transportable elements, for defense against viral sequences, and for transcriptional repression of certain genes. A strong suppression of the CpG methyl-acceptor site in human DNA results from mutagenic changes in 5-methylcytosine, causing C:G to T:A transitions. Normally, CpG islands, which are GC-rich evolutionarily conserved regions of more than 500 base pairs, are kept free of methylation. These stretches of DNA are located within the promoter region of about 40% of mammalian genes and, when methylated, cause stable, heritable transcriptional silencing. Aberrant de novo methylation of CpG islands is a hallmark of human cancers and is found early during carcinogenesis[14].

In addition to DNA methylation, histone modifications have also been found to have epigenetic effects. Acetylation and methylation of conserved lysine residues of the amino-terminal tail domains are the key elements in histone modification. Generally, the acetylation of histones marks active, transcriptionally competent regions, whereas hypoacetylation histones are found in transcriptionally inactive euchromatic and heterochromatic regions. On the other hand, histone methylation can be a marker for both active and inactive regions of chromatin. Methylation of lysine residue 9 on the N terminus of histone 3 (H3-K9) is a hallmark of silent DNA and is evenly distributed throughout the heterochromatic regions such as centromeres and telomeres, including the inactive Xchromosome. In contrast, methylation of lysine 4 of histone 3 (H3-K4) denotes activity and is predominantly found at promoter regions of active genes[15]. This constitutes a “histone code,” which can be read and interpreted by different cellular factors. There is evidence that DNA methylation depends on methylation of H3-K9 and can also be a trigger for its methylation. Recently, evidence has accumulated on the role of RNA in post-transcriptional silencing. In addition, RNA in the form of antisense transcripts (Xist or RNAi) can also lead to mitotically heritable transcriptional silencing by the formation of heterochromatin. For example, transcription of antisense RNA led to gene silencing and to the methylation of the structurally normal α-globin gene in patients with alpha thalassemia. This could be one of the many human diseases resulting from epigenetic silencing due to antisense RNA transcripts[16].

Mutations in genes that affect genomic epigenetic profiles can give rise to human diseases that can be inherited or somatically acquired (Table 20.4). These epigenetic mutations can be due either to hypermethylation (silencing) of a regulating gene or to loss of methylation (LOM) (activation) of another gene that has a positively modifying effect on the phenotype. The parental imprinting effect can be inferred by demonstrating the parental origin of the mutant allele. Similarly, either a loss or a gain of a chromosomal segment can result in the same situation. Confirmation of a specific chromosomal deletion or duplication is usually possible by using the fluorescent  insitu hybiridization (FISH) method. The paternal imprinting in this situation is commonly demonstrated by genotyping a set of polymorphic markers located within the chromosomal segment. Inheritance of the whole chromosomal homologue from one parent effectively confirms imprinting phenomenon, since the regulatory gene sequences for the pathogenic gene would be missing from the other parent. This characteristic abnormality is commonly referred to as “uni-parental disomy” or UPD. This could either be isodisomy (similar parental homologues) or heterodisomy (parental and grandparental homologues) (Figure 20.9). The origin of UPD is believed to result from the loss of the additional chromosomal homologue, failing which the conceptus would be trisomic. This mechanism is also called “trisomic rescue.”

Table 20.4 RECOGNIZABLE EPIGENETIC DYSMORPHIC SYNDROMES[12]  

DISEASE MAIN FEATURES EPIGENETIC  MECHANISM
ATR-X syndrome α-thalassemia, facial dysmorphic features, neurodevelopmental disabilities Mutations in ATRX gene; hypomethylation of repeat and satellite sequences
Fragile-X syndrome Chromosome instability, physical and learning/ behavioral difficulties Expansion and methylation of CGG repeat  in FMR1 5′ UTR, promoter  methylation
ICF syndrome Chromosome instability, immunodeficiency DNMT3 mutations; DNA  hypomethylation
Angelman syndrome Seizures and intellectual disabilities Deregulation of one or more imprinted genes at 15q11-13 (maternal)
Prader-Willi syndrome Obesity, intellectual disabilities Deregulation of one or more imprinted  genes at 15q11-13 (paternal)
Beckwith- Wiedemann (BWS) Organ overgrowth, childhood tumors Deregulation of one or more syndrome imprinted genes at 11p15.5 (IGF2, CDKN1C, KvDMR1,etc.)
Russel-Silver syndrome Growth delay, body asymmetry Deregulation of one or more imprinted  genes at 7p (maternal)
Rett syndrome Seizures, intellectual disabilities MeCP2 mutations
Rubinstein- Taybi syndrome Facial dysmorphism, intellectual disabilities Mutation in CREB-binding protein (histone acetylation)
Coffin- Lowry syndrome Facial dysmorphism, developmental delay
Mutation in RSk-2 (histone  phosphorylation)

 

Abbreviations: ATR-X—α-thalassemia, X-linked mental retardation; UTuntranslated region; ICFimmunodeficiency, chromosome instability, facial anomalies; CREB—cAMP-response-element- binding protein

For a maternally imprinted disorder, paternal UPD would be confirmatory and maternal UPD diagnostic for the paternally imprinted condition. For example, maternal UPD is diagnostic for Prader-Willi syndrome, and paternal UPD for Angelman syndrome, both conditions being associated with a microdeletion of the 15q11 region. The parental origin of the 15q microdeletion follows the expected epigenetic pattern and is in keeping with the clinical diagnosis. Recurrence risk estimates vary, depending on the specific epigenetic pattern. This information is crucial to obtain in order to offer accurate genetic counseling in any genomic imprinting disorder.

 

Figure 20.9 The origin of uniparental disomy 15 in Prader-Willi syndrome through trisomic rescue during early embryogenesisnote different homologues (maternal   heterodisomy).

Many epigenetic diseases are associated with chromosomal alterations and manifest with physical and learning difficulties. For example, mutations in X- linked mental retardation with the alpha thalassemia phenotype (ATRX) result in consistent changes in the methylation pattern of ribosomal DNA, Y- specific repeats, and subtelomeric repeats. Another X-linked recessive mental retardation syndrome, associated with a visible “fragile site” on the terminal part of the long arm of the X chromosome (fragile-X syndrome), results from de   novo   silencing   of   the   pathogenic   gene   FMR1.   The   syndrome  is characteristically associated with an abnormal expansion of CGG triplet repeats in the FMR1 5′ untranslated terminal region. Methylation of the expansion leads to silencing of the FMR1 gene and under certain cultural conditions creates the visible “fragile site” on the X chromosome.

Epigenetic silencing is probably also significant in other neurodevelopmental disorders. For example, in Rett syndrome, a common cause of intellectual disability in young girls, mutations of the MeCP2 gene are seen in about 80% of cases. The MeCP protein binds to methylcytosine residues and causes de-repression of genes normally suppressed by DNA methylation. Despite the lack of firm evidence, it is thought likely that MeCP2 might have a key role in the control of neuronal gene activity resulting in the pathology of Rett syndrome[17]. Interaction with another pathogenic gene (CTKL5 or STK9) in Rett syndrome is likely to be important in the pathogenesis of this neurodevelopmental disorder[18]. On a wider genomic level, mutations in the DNMT3b gene, causing the ICF (immunodeficiency, centromeric region instability, and facial anomalies) syndrome, result in deregulation of DNA methylation patterns. A notable example is that of Beckwith-Wiedemann syndrome (BWS), an overgrowth syndrome predisposing to Wilms’ tumor and other childhood tumors, which is associated with duplications and rearrangements of a small chromosomal region on the short arm of the chromosome (11p15.5). This region contains a cluster of genes, which is susceptible to a number of epigenetic alterations, manifesting with the BWS phenotype and tumorigenesis, particularly Wilms’ tumor and other childhood embryonal tumors (Figure 20.10). Loss of methylation in imprinting control regions (such as KvDMR1) can cause deregulation of imprinting, and either biallelic expression (IGF2 and H19) or silencing (such as CDKN1C) of imprinted genes, which is seen in most sporadic BWS cases[19].

The epigenetic phenomenon is probably significant for the phenotypical manifestations in some other hereditary tumors. For example, transmission of autosomal dominant familial chemodectomas (non-chromaffin paragangliomas or glomus tumors) is exclusively via the paternal line (Figure 20.11)[20]. The maternally derived gene is inactivated during oogenesis and can be reactivated only during spermatogenesis. This genetically heterogeneous cancer family syndrome is associated with germline mutations in succinate dehydrogenase subunits B (SDHB) and D (SDHD)[21].

Thus epigenetic changes are probably significant in a number of other complex phenotypes, particularly those associated with cancer and a number of degenerative diseases (see “Complex Genomic Diseases”).

DISORDERS OF GENOME ARCHITECTURE

Recent completion of the Human Genome Project and sequencing of the total genomes of yeast and other bacterial species have enabled investigators to view genetic information in the context of the entire genome. As a result, it is now possible to recognize mechanisms of some genetic diseases at the genomic level. Amongst the several biological processes, duplication of genes, gene segments, and repetitive gene clusters have helped in the evolution of mammalian genomes[22]. This aspect of genome architecture provides recombination hot spots between non-syntenic regions of chromosomes that are distributed across the whole genome. These genomic regions become susceptible to further DNA rearrangements that may be associated with an abnormal phenotype. Such disorders are collectively grouped under the broad category of “genome architecture disorders”[11].

Figure 20.10 The cluster of genes on 11p15.5 associated with the phenotype of Beckwith-Wiedemann syndrome. The methylated region KvDMR1 is indicated by the gray box within the gene KCNQ1OT1 and marked CH3 on the maternal homologue. The methylated region between the IGF2 and H19 genes is indicated by the hatched box and marked CH3 on the paternal homologue. With permission from Oxford University Press[23].

Figure 20.11 Pedigree showing paternal transmission of paraganglioma in a family: note no maternal transmission among “at-risk” family  members[20].

Table 20.5 CONTIGUOUS GENE SYNDROMES AS GENOMIC   DISORDERS[11]

Abbreviations: del—deletion; dup—duplication; inv—inversion; D—direct;   C—complex

Figure 20.12 Molecular mechanisms for genomic disordersdashed lines indicate either deleted or duplicated region; the rearranged genomic interval is shown in brackets; gene is depicted by filled horizontal rectangle; regulatory gene is shown as horizontal hash-marked rectangle; asterisks denote point mutations[24].

The term genome architecture disorder refers to a disease that is caused by an alteration of the genome that results in complete loss, gain, or disruption of the structural integrity of a dosage sensitive gene(s) (Figure 20.12). Notable examples include a number of chromosome deletion/duplication syndromes (Table 20.5). In these conditions, there is a critical rearranged genomic segment flanked by large (usually >10 kb), highly homologous low copy repeat (LCR) structures that can act as recombination  substrates. Meiotic recombination between non-allelic LCR copies, also known as non- allelic homologous recombination, can result in deletion or duplication of the intervening segment.

Similarly, other chromosomal rearrangements, including reciprocal, Robertsonian, and jumping translocations; inversions; isochromosomes; and small marker chromosomes, may also involve susceptibility to rearrangement related to genome structure or architecture. In several cases, LCRs, A-T–rich palindromes, and pericentromeric repeats are located at such rearrangement breakpoints. This susceptibility to genomic rearrangements is implicated  not only in disease etiology, but also in primate genome evolution[25].

An increasing number of Mendelian diseases (Table 20.6) are recognized to result from recurrent inter- and intra-chromosomal rearrangements involving unstable genomic regions facilitated by low-copy repeats (LCRs) [26]. These genomic regions are predisposed to non-allelic homologous recombination (NAHR) between paralogous genomic segments. LCRs usually span approximately 10–400 kb of genomic DNA, share 97% or greater sequence identity, and provide the substrates for NAHR, thus predisposing to rearrangements. LCRs have been shown to facilitate meiotic DNA rearrangements associated with several multiple malformation syndromes and some disease traits (Table 20.6). Seminal examples include microdeletion syndromes (Williams-Beuren syndrome[7q11del], DiGoerge syndrome[22q11del]); autosomal dominant Charcot-Marie-Tooth disease type 1A (PMP22 gene duplication); hereditary neuropathy of pressure palsy (HNPP: PMP22 gene deletion) mapped to 17p11.2; and Smith-Magenis, a contiguous gene syndrome (CGS) with del (17)(p11.2p11.2). Dominantly inherited male infertility related to AZF gene deletion follows a similar mechanism. In addition, this LCR-based complex genome architecture appears to play a major role in primate karyotype evolution, the pathogenesis of complex traits, and human carcinogenesis.

A notable example includes genetically heterogeneous Charcot-Marie- Tooth disease (CMTD). The disorder is also known as “hereditary motor and sensory neuropathy” (HMSN) by virtue of being a peripheral neuropathy due to involvement of either the axonal or myelinated segments of the peripheral nerve. Genetically autosomal dominant, autosomal recessive, and X-linked dominant types are recognized. The disorder is not uncommon, affecting approximately one in 2,500 of the adult population. This could be an underestimate, since medically the condition is benign, often not requiring any medical or surgical intervention. However, some affected individuals experience increasingly progressive neuromuscular weakness of distal muscles of lower legs, feet, distal forearms, and hands, with onset in the early teens, and causing severe locomotor restrictions.

An affected person usually presents late with relative hypertrophy of the upper calf muscles, described as an “inverted Champagne bottle”appearance (Figure 20.13), associated with pes cavus due to wasting of the small muscles of the feet. Similarly, wasting of the small muscles of hand leads to “clawhands.”  Neurophysiological  studies  remain  an  essential  method    of differentiating the two major types of CMTD. A reduced motor-nerve- conduction velocity of less than 35 m/sec helps in differentiating type 1 CMTD from type 2 CMTD, in which the motor-nerve-conduction velocity is usually normal but the sensory-nerveconduction is often slow. Whilst this distinction is undoubtedly helpful in determining clinical management, application for genetic counseling is limited because both types are genetically heterogeneous. For instance, molecular characterization and gene mapping have confirmed the existence of at least four types of type 1 CMTD: autosomal dominant types 1a, 1b, and 1c, and the X-linked type (XCMT). Similarly, there are distinct genetic types within the type 2 CMTD group.

Figure 20.13 Lower legs and feet in Charcot-Marie-Tooth diseasenote characteristic lower-leg appearance and pes cavus.

Table 20.6 MENDELIAN GENOMIC DISORDERS[11]

Abbreviations: del—deletion; dup—duplication; inv—inversion; D—direct; C—complex;   I—inverted

Figure 20.14 The 1.5 Mb duplicated chromosomal region of 17p12 including the PMP22 genenote 500 Kb junction fragment allele flanking the CMT1A gene detected by PFGE and Southern analysis. Note additional 17p segment (red color) by metaphase (top two pictures) and interphase (lower two pictures) FISH[11].

Approximately two-thirds of cases of CMT1 have a detectable 1.5 Mb duplication within a proximal chromosomal segment of the short arm of chromosome 17 (17p12)[27]. This duplicated chromosomal segment contains a gene for peripheral myelin protein called PMP22. This duplication  results in the disruption of the gene, leading to abnormal myelination of the peripheral nerves, an essential molecular pathological step resulting in the CMT1 phenotype designated as CMT1A. The CMT1A duplication was visualized  by  multiple  molecular  methods,  including  fluorescence  in-situ hybridization (FISH), pulsed-field gel electrophoresis (PFGE), and dosage differences of heterozygous alleles by restriction-fragment-length polymorphisms (RFLPs) (Figure 20.14). This finding led to further molecular studies on the origin of the 1.5 Mb duplicated 17p12 segment[28].

Figure 20.15 The unequal meiotic recombination (crossing-over) resulting in duplication (CMT1A) and deletion (HNPP)[11].

Studies by several investigators have revealed a significant variation in the size of marker alleles flanking the duplicated 17p12 region. It soon became apparent that a 500 kb allele co-segregated with 17p duplication in all affected individuals. This suggested a stable mutation and followed a precise recombination mechanism. However, in de novo duplication, the presence of repeated flanking marker alleles indicated the mechanism of unequalcrossing- over leading to duplication. Indeed, this was confirmed when a highly homologous >20 kb–size repeat sequence was confirmed flanking the 17 p duplication. It was appropriately named “CMT1A-REP.” As predicted by the unequal crossing-over model, CMT1A-REP was found to be present in three copies on the CMT1A duplication-bearing chromosome. Interestingly, the presence of only one copy was soon demonstrated in another peripheral nervous system disorder, known as “hereditary neuropathy with liability to pressure” (HNPP)[29]. Most clinically affected individuals with HNPP present with mild to moderate episodic weakness of the lower limbs and occasionally of upper limbs when subjected to prolonged pressure, such as sitting or sleeping. The disorder is dominantly inherited in an autosomal dominant manner. This is generally a clinically mild and benign hereditary neuropathy. The presence of only one copy results from a reciprocal deletion following unequal crossing-over involving the CMT1A-REP repeat (Figure 20.15).

Similar  observations  were   also   made   in   relation  to   Smith-Magenis syndrome (SMS), a contiguous gene syndrome associated with a microdeletion of the 17p11.2 segment (Greenberg et al. 1991). Affected children present with facial dysmorphic features, severe speech delay, and behavioral problems, with signs of self-harm. A specific junction fragment was detected by PFGE (SMS-REP) that was involved in recurrent rearrangement resulting in either SMS or reciprocal 17p11.2 duplication. Pathogenic mutations in RAI1 gene, mapped to the 17p11.2 chromosomal region, are now shown to be etiologically linked with SMS[18]. It is also possible to have both duplication and deletion at the same time, resulting from DNA rearrangements on both homologues of chromosome 17. This was demonstrated in a patient with mild delay and a family history of autosomal dominant carpel-tunnel syndrome[30]. The occurrence of both the 17p11.2 duplication and the HNPP deletion in this patient reflects the relatively high frequency at which these abnormalities arise and the underlying molecular characteristics of the genome in this region.

It is perfectly reasonable to accept the argument that similar molecular mechanisms apply in causing other disorders (Table 20.6). The human genome has evolved an architecture that may make us as a species more susceptible to rearrangements causing genomic disorders[28].

DISORDERS WITH TRI-NUCLEOTIDE (TRIPLET)  REPEATS

Several disorders are recognized to have a phenomenon of earlier age-at- onset of disease in successive generations. This is known as “anticipation.” This observation failed to secure a valid biological explanation and had been put aside simply on the basis of biased ascertainment of probands or random variations in the age of onset. With the identification of unstable  DNA repeats distributed across the genome, a molecular basis has been found for the phenomenon of anticipation. These unstable DNA repeats tend to increase in size during meiosis over successive generations. The abnormal expansion is correlated with reducing age of onset and increased severity with further expansion of DNA repeats. The characteristic pattern of the DNA repeat involving a set of three nucleotides is commonly referred to “tri-nucleotide” or “triplet” repeats[31]. This soon became established as a novel class of mutation, and it offered a plausible explanation for the phenomenon of anticipation and variable clinical severity in a number of neurodegenerative diseases (Table 20.7).

Figure 20.16 Location of four classes of triplet repeats in human diseases. Exons are shown in light pink with intervening introns as a pink solid line. The translation site AUG and termination signal TAA are indicated by red vertical bars. Adapted with permission from Principles of Medical Genetics by Thomas  D.  Gelehrter, Francis S. Collins, and David Ginsburg[1].

Table 20.7 DISORDERS WITH TRINUCLEOTIDE (TRIPLET) REPEAT EXPANSION[11]

Abbreviation:  UTR—untranslated region

The X-linked recessive spinal bulbar atrophy (SBA) was one of the first hereditary neurological disorders recognized to be associated with CAG triplet repeats. The expanded region can occur anywhere in the gene and thus can disrupt the expression of the gene. In the case of X-linked fragile-X syndrome (FRAXA), the CGG repeats are found in the 5′-untranslated region of the first exon of FMR1, the pathogenic gene for FRAXA (Figure 20.16). However, in the case of Friedreich’s ataxia (FA), an autosomal recessive form of spinocerebellar ataxia (SCA), the expanded triplet repeat allele (GAA) occurs in the first intron of X25, the gene encoding frataxin. In Huntington disease (HD) and other inherited neurodegenerative disorders, the CAG triplet repeats occur within exons and encode an elongated polyglutamine tract (Figure 20.17). However, the expanded CTG triplet repeats of myotonic dystrophy (DM) are found in the 3′-untranslated  region of the last exon of the DM protein kinase (myotonin) gene (DM).

Each class of trinucleotide repeats exists in normal individuals. A pathogenic expansion is the one that is seen in clinically symptomatic individuals. Carriers for an X-linked disease also have an expanded allele (pre-mutation), which does not usually result in an abnormal phenotype. However, it is likely that some carrier females might exhibit some manifestations as in fragile-X syndrome. An expanded allele in the pre- mutation range in a male would not be associated with any clinical manifestations (normal transmitting male NTM), but this could further expand, resulting in all his daughters’ being carriers. However, recent studies have provided data on the existence of late-onset gait ataxia in NTMs[32]. On the other hand, a normal-size CGG repeat in a normal male could undergo further expansion during meiosis, leading to a carrier daughter. This usually comes to light when a symptomatic grandson is confirmed to have pathogenic FRAXA expansion. Prior to availability of the molecular testing in FRAXA, this kind of unusual pedigree pattern in fragile-X syndrome was called the “Sherman paradox” (Figure 20.18). Detailed molecular studies in the family are often necessary to offer accurate genetic counselling to “at-risk” carrier females. Carrier females are at an additional risk for developing premature ovarian failure, usually diagnosed when investigated for secondary infertility (see Chapter 46).

 

Figure 20.17 Schematic diagram of the polyglutamine tract resulting from abnormal expansion of CAG trinucleotide repeats[33].

Figure 20.18 The Sherman paradox: a hypothetical pedigree showing affected members (red) and carrier females (pink); individual III.1 is a normal transmitting male; the % risk for mental retardation is given for respective size of the triplet (CGG) repeats. Adapted with permission from Principles of Medical Genetics by Thomas D. Gelehrter, Francis S. Collins, and David Ginsburg[1,2].

Figure 20.19 The Sherman paradox: a hypothetical pedigree showing affected members (red) and carrier females (pink); individual III.1 is a normal transmitting male; the % risk for mental retardation is given for respective size of the triplet (CGG) repeats. (Fu et al.,  1991)

Genetic counselling in other neurodegenerative disorders with triplet repeats is often complicated. In particular, the clinical prediction in “borderline” expanded triplet repeats (intermediate allele) in HD is extremely difficult due to lack of reliable data. However, recent studies have produced some data that are likely to be helpful in genetic counselling.

COMPLEX GENOMIC DISEASES

All inherited disorders have a genetic abnormality present in the DNA of all cells in the body, including germ cells (sperm and egg), and can be transmitted to subsequent generations. In contrast, a genetic abnormality present only in specific somatic cells could not be transmitted. The genetic abnormality in a somatic cell can occur any time from the post-conception stage to late adult life. The paradigm of somatic cell genetic  disorder is cancer, where the development of malignancy is often the consequence of mutations in genes that control cellular growth. There are several such genes, and these are designated oncogenes. It is now accepted that all human cancer results from mutations in the nuclear DNA of a specific somatic cell, making it the most common genetic disease. The various genetic mechanisms  that can result in cancer are discussed in the chapter on cancer genomics (see Chapter 36).

The clinical course and outcome of treatment in a number of acute and chronic medical conditions depend upon various factors. For instance,  there is overwhelming evidence that highly polymorphic cytokine, interferon, and interleukin families of complex proteins influence the host’s  response to acute infection and physical injury or inflammation. Several genes encode these inflammatory pathway proteins. Similarly, association of human leucocyte antigens in the pathogenesis of a number of acute and chronic medical disorders is well known (see Chapter 38). In addition, interaction of mutations within these genes and with several other genomic polymorphisms, such as single-nucleotide polymorphisms (SNPs) is probably important in several acute medical conditions, including trauma. This will have a major impact in critical care and acute medicine (see Chapter 48). The role of SNPs in modulating complex medical disorders, such as diabetes mellitus, coronary heart disease, hypertension, and various forms of cancer,  is unclear. However, the complexity of interaction of SNPs with other genetic traits and loci is probably important in the prognosis of these disorders, in particular the outcome of therapeutic interventions. This argument probably justifies separating some of these disorders under the title of “complex genomic diseases.”

Figure 20.20 Schematic diagram of the polyglutamine tract resulting from abnormal expansion of CAG trinucleotide repeats. Adapted from Perutz et al., 1994, with permission.

Various cancers and degenerative diseases occur with increasing frequency in old age. However, these may also present at a younger age, such as childhood leukemias. The molecular mechanisms in these diseases are not entirely clear, but probably include defects in DNA repair mechanisms, accelerated apoptosis, deregulation of imprinted genomic regions, and de novo chromosome rearrangements involving specific genomic regions. Although these disorders can be arguably included under the broad category of “multi-factorial/polygenic diseases,” the pattern of distribution and recurrence does not follow the agreed principles of multi-factorial/polygenic inheritance as discussed elsewhere in this chapter.

As described in the previous section on epigenetics, epigenetic changes play a major role in the development of human cancer[12]. A high percentage of patients with sporadic colorectal cancer (CRC) possess microsatellite instability and show methylation and silencing of the gene encoding  MLH1. It is thus likely that epigenetic changes also predispose to genetic instability. In some cases, promoter-associated methylation of MLH1 is found not only in the tumor, but also in normal somatic tissues, including spermatozoa. These germline “epimutations” predispose individuals carrying abnormal methylation patterns to multiple cancers. Indeed, disruption of pathways that lead to cancer is often caused by the de novo methylation of the relevant gene’s promoters[14]. Epigenetic silencing has been recognized as a third pathway satisfying Knudson’s “two-hit” hypothesis for the silencing of tumor-suppressor genes[34].

Chromosomal rearrangements have long been associated with human leukemias. These result in the formation of fusion proteins, including histone acetyltransferases and histone methyltransferases, that influence upregulation of target genes. In acute promyelocytic leukemia, the oncogenic fusion protein PML-RARα (promyelocytic leukemia–retinoic acid  receptor-α) causes the repression of genes that are essential for the differentiation of hematopoietic cells. Similarly, in acute myeloid leukemia, AML-ETO fusions recruit the repressive N-COR-Sin3-HDAC1 complex and inhibit myeloid development[35]. There are further examples of complex genomic arrangements that result in other cancers, and that can modify the therapeutic response. For example, mutations in genes for ATPase  complex are associated with poorer prognosis in patients with non–smallcell lung cancer[36].

DISEASE SPECTRUM, BIOLOGICAL PATHWAYS,AND GENOTYPES

In modern medicine, diagnosis of any disease or morbid state relies on establishing the phenotype along the lines of agreed parameters (Table 20.8). The next logical step is to find evidence for likely  pathophysiological changes that could be logically linked with one or more phenotypes. This could be demanding and challenging, as it might involve in-depth analysis and understanding of the complex biological (e.g., metabolic or molecular) pathways implicated in the disease process (Table 20.9). Once this was achieved, then a correlation could be looked for with specific protein or enzyme systems recognized to be essential component(s) of the core and successive biological pathways. Finding structural or  functional abnormalities of any given protein or enzyme system would require undertaking investigations targeted at specific gene(s) or genomic regions harboring particular gene(s). Establishing the precise genotype would then be the final piece in the complex jigsaw puzzle that is collectively labeled as a disease or syndrome. The individual genotype could be in any form (Table 20.8,III) including gross chromosomal changes, specific genes or gene clusters, and extremely small segments of the genome. Thus the whole landscape of the disease or diagnosis involves a closely linked network of three domains in the order of genotype–pathway–phenotype. In other words, a diagnosis of any disease or morbid state (including the mortal state) would be a cumulative process that should take into account all three of these domains: disease= genotype + molecular pathway + genotype.

Table 20.8 TAXONOMY OF HUMAN DISEASE: CORRELATION OF CLINICAL PHENOTYPES, MOLECULAR PATHWAYS, AND  GENOTYPES

I: Phenotypes:

Clinical—symptoms and physical  signs

I: Correlation and interpretation of the above with one or more of the following parameters wit the aim of arriving at a diagnosis or most likely underlying mechanism of the   disease:

Biochemical; e.g., urea/electrolytes, blood gases Metabolic; e.g., sugar/lipid/endocrine  profiles

Radiological—X-rays, ultrasound, CT/MRI scans, magnetic resonance spectroscopy, radioisotope, etc.

Pathological—histopathology, histochemistry, immune-histology, fluorescence microscopy, and electron microscopy

Hematological—hemoglobin, hematocrit, coagulation profile,  etc.

Immunological—immunoglobulins (IgG, IgM, IgA, etc.); antibody profiles, e.g., lupus; specific immunological investigation

Microbial/ Pathogens—battery of tests for bacterial, viral, protozoal, parasitic, and fungal infections, including specific pathogen  profiles

Toxicology—poisons, alcohol, therapeutic and recreational  drugs

Environmental (Ecological)—Temperature extremes, high altitude, supersonic flying, and space travel

II: Correlation of the above phenotypes with one or more of the biological/ molecular   pathways:

Growth factors/ growth factor receptors (e.g., EGF/EGFRs, FGF/FGFRs, TGF/TGFRs,and VGF/VGFRs)

Dynamic cell/tissue factors (e.g., protein kinase families such as P13, RAS/MAPK; tumor suppressor systems, etc.)

Respiratory chain/ oxidative pathways (e.g., mitochondrial and cyclooxygenase   systems)

Cell/ tissue response systems (e.g., cytokines, interleukins, tissue necrosis factors, complement factors, etc.)

Apoptosis/ senescence systems (e.g., apoptotic  pathways)

Scavenger/ housekeeping systems (e.g., lysosomal enzymes, alpha 1 antitrypsin, DNA repair genes, etc.)

Metabolic regulatory systems (e.g., insulin/glycemic regulation, lipids/ hepato-biliary systems, Krebs cycle, etc.)

Energy regulation (e.g., temperature regulation, energy conservation, nutritional state, etc.) Hormonal regulation (e.g., endocrine pathways, autocrine and paracrine   pathways)

Vascular pathways (e.g., angiogenetic systems, clotting/ coagulation pathways, and platelet factors)

III: Correlation and/or interpretation with ALL of the above with one (or more) individual’s genetic/ genomic pathology:

Chromosomal aberration—aneuploidy (e.g., trisomy 21, 18, 13; triploidy); structural changes (micro-deletion/duplication, inversion, ring chromosome,  etc.)

OR

Specific gene mutations in a Mendelian disorder (e.g., betal thalassemia, cystic fibrosis, Duchenne muscular dystrophy)

OR

Mutations in 2 or more genes (oligo- or multigenic) belonging to a gene/ molecular family (e.g., sarcomere genes in hypertrophic  cardiomyopathy)

OR

Interaction of several hundreds and thousands of low risk alleles/genes with one or more environmental factors, including the lifestyle—polygenic/  multifactorial

OR

Mitochondrial gene mutations and/or polymorphisms—several multisystem disorders that follow matrilineal inheritance pattern.

Table 20.9 GENETIC AND GENOMIC PATHOLOGY IN HUMAN DISEASE

The following genetic/ genomic pathology might be associated with one or more clinical phenotypes. Interpretation and precise diagnosis would depend on the natural history, family history, and sensitivity/ specificity of genetic/genomic  analyses:

•  Epigenetic/ epigenomics changes—mutations/ deletions/ duplication/ inversion of genes or genomic segments adjacent to the promoter region of certain genes; genetic imprinting abnormality involving specific genes demonstrating “parent of origin effect,” including complete, partial, or mosaic uniparental disomy.

•  Genome-wide abnormalities—pathogenic or disease-modification effect of structural variation across the genome; for example, single-nucleotide polymorphisms, copy number variations, deletions/ duplications, nucleotide repeats (e.g., trinucleotide repeats).

•  Gene function/ expression—specific “gain of function” or “loss of function” gene mutations (e.g., increased risk of cancer/tumor due to mutation in a tumor-suppressor gene);  mutations in transcription factors associated with a range of developmental anomalies; abnormalities in RNA interference system associated with exaggerated or blunted therapeutic response; post- translational modification/ changes in the gene product associated with one or more  phenotypes consistent with a disease diagnosis.

SUMMARY

Developments in genetics and subsequently the sequencing of the human genome have provided us with an opportunity to review the taxonomy of human disease. Conventionally, the causation of human disease includes malformations, trauma, infection, immune dysfunction, metabolic abnormality, malignancy, and degenerative conditions associated with aging. Genetic factors have long been recognized in all of these disease groups. The traditional genetic categories of diseases include chromosomal disorders, single-gene or Mendelian diseases, and several forms of multifactorial/polygenic conditions. In addition, somatic genetic changes and mutations of the mitochondrial genome probably account for a small, albeit important, number of diseases. These groups of disorders are well recognized and have an established place in the classification of human disease.

Recent developments in genome research have provided a wealth of data indicating different genomic mechanisms to explain complex pathogenesis in some disorders. The spectrum of these disorders is wide and includes both acute and chronic medical and surgical diseases. Perhaps it is reasonable to identify these disorders on the basis of their underlying molecular pathology, including genomic imprinting, genomic rearrangements, and gene– environment interactions involving multiple genes and genomic polymorphisms. This chapter has reviewed the genetic and genomic approaches in the classification of human disease. A stepwise approach is presented based on correlations of the clinical phenotype, supporting investigative phenotypes and specific evidence from targeted genetic and genomic analyses. This approach would enable a modern clinician to finally arrive at the final determining factor in the causation of human disease. The new taxonomy of human disease is likely to have a major impact on the practice of clinical medicine in the future.

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KNOWLEDGE BASE
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